The answer was either significantly limit the amount of flasks you can take in a fight to actually make challenging bosses, significantly reduce the healing from flasks if you chain chug them within a short period, or give them actual good and aggressive AI that prevents the player from healing.
I don't disagree and was actually surprised when I heard that ER carried over the flask system at all. Due to the open world setup and exploration, this is the one time where the single-use healing items (and subsequent farming when you run dry) from Demon's or Bloodborne would have made perfect sense.
Farming? Heck no, this games crafting system is poor enough as it is. Farming would be only for increasing your slots - like OK, you got a recipe for your next ritual pot from the traveling merchant in the new area, go collect these ingredients and he'll give you another pot that you select just like the type of flasks, and then at bonfire you refill it. The pots in this game outside the sleeping pot for enemies vulnerable just feel weak and not worth the trouble it takes to get the ingredients because they just feel wasted on normal enemies, and just aren't effective against bosses unless they're uniquely vulnerable to a particular ailment.
The healing/mana flasks on the same number of charges was an OK system as it at least forces you to make meaningful choices between FP and health, but I wish they'd taken it a step further with bosses, and did something like made boss flasks take up MUCH a more limited number of slots, or make each flask take up more weight so you're having to make a tradeoff between taking more healing, and more mitigation.
Honestly when being summoned, the flasks being cut in half is actually a pretty good balance point for a lot of bosses at appropriate soul level. I have NEVER run out of flasks fighting my own boss whether that's solo, with ash summons, or sunbro summons. But in some of the fights if summoned at a reasonably appropriate level, you DO have to actually take healing into account, and may actually run out if you're running a high FP cost build or playing the tank for a mage/squishy melee. They simply gave you way too much healing and FP restore in the regular game.
Although I DID think that the Raw Meat Dumpling was a huge wasted opportunity (disregarding how broken it is on Mimic if you feel like cheesing bosses) - that would have been a legitimately interesting system of healing for debuff. Every time you chug a flask it increases the level of a debuff like Poison, reduces your damage/stamina, etc. Force the player to make a meaningful tradeoff for constantly chugging up flasks in a boss fight, and possibly alter their playstyle if forced to take too many to try and avoid the negatives, instead of just piling on chunks of damage trying to make them use all of them.